load Brgo.v3.0anno.Atgoslim.BP.list

load(file.path("..","Annotation_copy","output","v3.0annotation","Brgo.v3.0anno.Atgoslim.BP.list.Rdata"))

load GO.ORA function

GOseq function for Brassica rapa (v3.0)

# GOseq
library(ShortRead);library(goseq);library(GO.db);library("annotate")
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## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.
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## Loading required package: XML
# for ggplot heatmap
## uncompress gz file
system(paste("gunzip -c ",file.path("..","Annotation_copy","input","v3.0annotation","Brapa_genome_v3.0_cds.gz")," > ",file.path("..","Annotation_copy","input","v3.0annotation","Brapa_genome_v3.0_cds.fa")))
## read cDNA fasta file 
Bra.v3.0_cdna<-readDNAStringSet(file.path("..","Annotation_copy","input","v3.0annotation","Brapa_genome_v3.0_cds.fa")) # copied from /Volumes/data_work/Data8/NGS_related/Brassica_rapa_Upendra/G3
Bra.v3.0_cdna
##   A DNAStringSet instance of length 46250
##         width seq                                           names               
##     [1]  1254 ATGCGACCACCGGGTGTTGTT...GAGTCTCTCTTGCTCGCTTAA BraA01g000010.3C
##     [2]  1668 ATGCCAGCAATGCATGCCGTT...AGATGGATCACAAAAGATTAA BraA01g000020.3C
##     [3]   957 ATGATGCTTCTCGTTCATACC...AACTTGGAGTTCCCTGAGTGA BraA01g000030.3C
##     [4]  1299 ATGAGTCGTCTTCTCCTTGCT...GGGTCACGAGATGAGCTATAA BraA01g000040.3C
##     [5]   774 ATGGATTCTGGGCTTCAGCAT...GGAAAGCAGTTCCTTTCGTGA BraA01g000050.3C
##     ...   ... ...
## [46246]   162 ATGCGTCCGTCCTCAGCTCCC...TCTTTGGTGGTCCGGTTCTAA BraAnng001840.3C
## [46247]  1455 ATGTCTAATCAAGGATCAGGA...ACAGGTTTGTTTAGGTGCTAA BraAnng001850.3C
## [46248]  1011 ATGGACAACGTAATTCTGAAA...TCAGGGAAGAAAAGCCCCTGA BraAnng006150.3C
## [46249]   870 ATGTTTCCAAGACGTACAAGG...AGCAGTTGTCCTTATAGTTAG BraAnng000040.3C
## [46250]  1338 ATGCCGCAACAATACTGGAAC...GGAGAGAACCTTATCTCCTGA BraAnng003440.3C
## remove fasta file
system(paste("rm ",file.path("..","Annotation_copy","input","v3.0annotation","Brapa_genome_v3.0_cds.fa"),sep=""))
# GOseq function
GOseq.Brgo.v3.0.Atgoslim.BP.list.ORA<-function(genelist,padjust=0.05,ontology="BP",custom.category.list=Brgo.v3.0anno.Atgoslim.BP.list,Br_cdna=Bra.v3.0_cdna) { # return GO enrichment table, padjus, padjust=0.05. 
  
  bias<-nchar(Br_cdna)
  names(bias)<-names(Br_cdna)
  TF<-(names(bias) %in% genelist)*1
  names(TF)<-names(bias)
  #print(TF)
  pwf<-nullp(TF,bias.data=bias)
  #print(pwf$DEgenes)
  GO.pval <- goseq(pwf,gene2cat=custom.category.list,use_genes_without_cat=TRUE) # format became different in new goseq version (021111). Does not work (042716)
  #GO.pval <- goseq(pwf,gene2cat=Brgo.DF3,use_genes_without_cat=TRUE) # format became different in new goseq version (021111)
  
  #head(GO.pval) 
  if(ontology=="BP") {
    GO.pval2<-subset(GO.pval,ontology=="BP")
  } else if(ontology=="CC") {
    GO.pval2<-subset(GO.pval,ontology=="CC")
  } else {
    GO.pval2<-subset(GO.pval,ontology=="MF")
  }
    
  GO.pval2$over_represented_padjust<-p.adjust(GO.pval2$over_represented_pvalue,method="BH")
  if(GO.pval2$over_represented_padjust[1]>padjust) return("no enriched GO")
  else {
    enriched.GO<-GO.pval2[GO.pval2$over_represented_padjust<padjust,] 
    print("enriched.GO is")
    print(enriched.GO)
    
    ## write Term and Definition 
    for(i in 1:dim(enriched.GO)[1]) {
      if(is.null(Term(GOTERM[enriched.GO[i,"category"]]))) {next} else {
      enriched.GO$Term[i]<-Term(GOTERM[[enriched.GO[i,"category"]]])
      enriched.GO$Definition[i]<-Definition(GOTERM[[enriched.GO[i,"category"]]])
      }
    }
    return(enriched.GO)
  }
}
#
head(Bra.v3.0_cdna)
##   A DNAStringSet instance of length 6
##     width seq                                               names               
## [1]  1254 ATGCGACCACCGGGTGTTGTTTC...CTGAGTCTCTCTTGCTCGCTTAA BraA01g000010.3C
## [2]  1668 ATGCCAGCAATGCATGCCGTTTT...GTAGATGGATCACAAAAGATTAA BraA01g000020.3C
## [3]   957 ATGATGCTTCTCGTTCATACCCG...GGAACTTGGAGTTCCCTGAGTGA BraA01g000030.3C
## [4]  1299 ATGAGTCGTCTTCTCCTTGCTCA...GTGGGTCACGAGATGAGCTATAA BraA01g000040.3C
## [5]   774 ATGGATTCTGGGCTTCAGCATCT...AAGGAAAGCAGTTCCTTTCGTGA BraA01g000050.3C
## [6]  3327 ATGGCGTCCACTCCTCCTCAAAA...GCGGTGGGTTTCAATTTCCTTGA BraA01g000060.3C
# length(bias) # 44239 > 45019 where the bias come from?
#  bias.data vector must have the same length as DEgenes vector!

ORA: two afternoon and expression pattern

twoafternoon.trtlive.DEGs.all.v3.0anno<-read_csv(file=file.path("..","output","twoafternoon.trtlive.DEGs.all.v3.0anno.csv"))
## Parsed with column specification:
## cols(
##   genes = col_character(),
##   logFC = col_double(),
##   logCPM = col_double(),
##   LR = col_double(),
##   PValue = col_double(),
##   FDR = col_double(),
##   AGI = col_character(),
##   At_symbol = col_character(),
##   At_short_description = col_character(),
##   perc_ID = col_double()
## )
  library(dplyr)
  #genelist.up<-base::get(paste("../output/",DEG.objs.v3.0annotation.unique[n],sep="")) %>% rownames_to_column() %>%  dplyr::filter(logFC>0) # does not work
    temp<-twoafternoon.trtlive.DEGs.all.v3.0anno
    genelist.up<-temp[temp[,3]>0&temp[,"FDR"]<0.05,"genes"];genelist.down<-temp[temp[,3]<0&temp[,"FDR"]<0.05,"genes"]
   print(paste("number of up genes is ",dim(genelist.up)[1]))
## [1] "number of up genes is  1416"
  # expression pattern of upregulated genes
   gene.of.interest.FDR.up <- twoafternoon.trtlive.DEGs.all.v3.0anno %>% filter(FDR< 0.05,logFC>0) %>%
     dplyr::select(genes,logFC,FDR) %>% arrange(FDR)
   print("logFC>0")
## [1] "logFC>0"
   p.up1<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[1,]);p.up1
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector
## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

   p.up2<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[2,]);p.up2
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector

## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

   p.up3<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[3,]);p.up3
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector

## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

   p.up4<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[4,]);p.up4
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector

## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

   p.up5<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.up[5,]);p.up5
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector

## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

  # expression pattern of diwbregulated genes
   gene.of.interest.FDR.down <- twoafternoon.trtlive.DEGs.all.v3.0anno %>% filter(FDR< 0.05,logFC<0) %>% dplyr::select(genes,logFC,FDR) %>% arrange(FDR)
   print("logFC<0")
## [1] "logFC<0"
   p.down1<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[1,]);p.down1
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector

## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

   p.down2<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[2,]);p.down2
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector

## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

   p.down3<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[3,]);p.down3
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector

## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

   p.down4<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[4,]);p.down4
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector

## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

   p.down5<-expression.pattern.Br.graph.timecourse.v3.0annotation.cpm(target.genes.FDR=gene.of.interest.FDR.down[5,]);p.down5
## Warning: Column `sample` joining character vector and factor, coercing into
## character vector

## Warning: Column `target_id`/`genes` joining factor and character vector,
## coercing into character vector

    #genelist.down<-read_csv(paste("../output/",file,sep=""))  %>%  dplyr::filter(logFC.genotypeR500<0)
   if(dim(genelist.up)[1]<3) {print("Number of up genes is smaller than three. Skip this."); GO.ORA.temp.up<-"no enriched GO";next} else {GO.ORA.temp.up<-GOseq.Brgo.v3.0.Atgoslim.BP.list.ORA(as_vector(genelist.up)) }
## Warning in pcls(G): initial point very close to some inequality constraints
## Using manually entered categories.
## Calculating the p-values...
## 'select()' returned 1:1 mapping between keys and columns

## [1] "enriched.GO is"
##        category over_represented_pvalue under_represented_pvalue numDEInCat
## 1210 GO:0010200            1.357094e-12                1.0000000         36
## 2253 GO:0042742            1.061509e-10                1.0000000         61
## 890  GO:0009611            9.615647e-09                1.0000000         39
## 2750 GO:0050832            2.163094e-08                1.0000000         39
## 899  GO:0009626            3.350053e-08                1.0000000         21
## 638  GO:0006952            7.956456e-08                1.0000000         75
## 853  GO:0009407            7.000843e-07                0.9999999         11
## 900  GO:0009627            9.893457e-07                0.9999998         15
## 1174 GO:0010120            2.987504e-06                0.9999998          8
## 894  GO:0009617            3.027497e-06                0.9999991         24
## 557  GO:0006749            4.127199e-06                0.9999994         12
## 646  GO:0006979            4.499773e-06                0.9999982         36
## 3708 GO:2000022            5.272435e-06                0.9999991         13
## 1166 GO:0010112            5.493947e-06                0.9999996          7
## 423  GO:0006468            6.010503e-06                0.9999967         91
## 2859 GO:0051707            1.635476e-05                0.9999968         13
## 972  GO:0009751            1.886256e-05                0.9999932         27
## 1038 GO:0009871            1.984908e-05                0.9999993          5
## 3442 GO:1900067            4.006062e-05                1.0000000          3
## 1107 GO:0010030            4.605592e-05                0.9999934          9
## 855  GO:0009409            5.161047e-05                0.9999755         42
## 3164 GO:0071732            5.481625e-05                0.9999920          9
## 898  GO:0009625            6.533906e-05                0.9999874         11
## 1858 GO:0031348            9.920065e-05                0.9999821         10
## 3114 GO:0071369            1.327728e-04                0.9999777          9
## 607  GO:0006869            1.391666e-04                0.9999608         15
## 2986 GO:0062034            1.434714e-04                0.9999954          4
## 1183 GO:0010150            1.702460e-04                0.9999427         19
## 2917 GO:0055114            1.965588e-04                0.9998735         96
## 49   GO:0000272            2.534934e-04                0.9999663          7
## 921  GO:0009651            2.650096e-04                0.9998502         56
## 2439 GO:0045332            2.706706e-04                0.9999723          6
## 478  GO:0006562            2.881153e-04                0.9999969          3
## 185  GO:0002229            3.712637e-04                0.9998926         14
## 3094 GO:0071281            4.180861e-04                0.9999083         10
##      numInCat
## 1210      286
## 2253      726
## 890       419
## 2750      469
## 899       140
## 638      1165
## 853        67
## 900       104
## 1174       27
## 894       241
## 557        85
## 646       502
## 3708       89
## 1166       22
## 423      1484
## 2859       97
## 972       347
## 1038       11
## 3442        3
## 1107       54
## 855       696
## 3164       52
## 898        84
## 1858       64
## 3114       62
## 607       208
## 2986        8
## 1183      219
## 2917     1923
## 49         39
## 921      1045
## 2439       23
## 478         4
## 185       126
## 3094       77
##                                                                                               term
## 1210                                                                            response to chitin
## 2253                                                                 defense response to bacterium
## 890                                                                           response to wounding
## 2750                                                                    defense response to fungus
## 899                                                             plant-type hypersensitive response
## 638                                                                               defense response
## 853                                                                        toxin catabolic process
## 900                                                                   systemic acquired resistance
## 1174                                                                camalexin biosynthetic process
## 894                                                                          response to bacterium
## 557                                                                  glutathione metabolic process
## 646                                                                   response to oxidative stress
## 3708                                        regulation of jasmonic acid mediated signaling pathway
## 1166                                                    regulation of systemic acquired resistance
## 423                                                                        protein phosphorylation
## 2859                                                                    response to other organism
## 972                                                                     response to salicylic acid
## 1038 jasmonic acid and ethylene-dependent systemic resistance, ethylene mediated signaling pathway
## 3442                                                regulation of cellular response to alkaline pH
## 1107                                                       positive regulation of seed germination
## 855                                                                               response to cold
## 3164                                                             cellular response to nitric oxide
## 898                                                                             response to insect
## 1858                                                       negative regulation of defense response
## 3114                                                        cellular response to ethylene stimulus
## 607                                                                                lipid transport
## 2986                                                         L-pipecolic acid biosynthetic process
## 1183                                                                               leaf senescence
## 2917                                                                   oxidation-reduction process
## 49                                                                polysaccharide catabolic process
## 921                                                                        response to salt stress
## 2439                                                                    phospholipid translocation
## 478                                                                      proline catabolic process
## 185                                                                  defense response to oomycetes
## 3094                                                                 cellular response to iron ion
##      ontology over_represented_padjust
## 1210       BP             5.142029e-09
## 2253       BP             2.011029e-07
## 890        BP             1.214456e-05
## 2750       BP             2.048991e-05
## 899        BP             2.538670e-05
## 638        BP             5.024502e-05
## 853        BP             3.789456e-04
## 900        BP             4.685789e-04
## 1174       BP             1.147119e-03
## 894        BP             1.147119e-03
## 557        BP             1.420803e-03
## 646        BP             1.420803e-03
## 3708       BP             1.486897e-03
## 1166       BP             1.486897e-03
## 423        BP             1.518253e-03
## 2859       BP             3.873011e-03
## 972        BP             4.178232e-03
## 1038       BP             4.178232e-03
## 3442       BP             7.988931e-03
## 1107       BP             8.725295e-03
## 855        BP             9.312003e-03
## 3164       BP             9.440854e-03
## 898        BP             1.076390e-02
## 1858       BP             1.566130e-02
## 3114       BP             2.012305e-02
## 607        BP             2.013382e-02
## 2986       BP             2.013382e-02
## 1183       BP             2.303794e-02
## 2917       BP             2.568143e-02
## 49         BP             3.201621e-02
## 921        BP             3.204910e-02
## 2439       BP             3.204910e-02
## 478        BP             3.308087e-02
## 185        BP             4.137407e-02
## 3094       BP             4.526081e-02
      print(paste("number of down genes is ",dim(genelist.down)[1]))
## [1] "number of down genes is  58"
   if(dim(genelist.down)[1]<3) {print("Number of up genes is smaller than three. Skip this."); GO.ORA.temp.down<-"no enriched GO"; next} else {GO.ORA.temp.down<-GOseq.Brgo.v3.0.Atgoslim.BP.list.ORA(as_vector(genelist.down)) }
## Using manually entered categories.
## Calculating the p-values...
## 'select()' returned 1:1 mapping between keys and columns

    # handling "no enriched GO" 
    # genelist.names<-c("GO.ORA.temp.up_down","GO.ORA.temp.down_up") # test
    x<-list(GO.ORA.temp.up=GO.ORA.temp.up,
            GO.ORA.temp.down=GO.ORA.temp.down) # list
    x<-x[!x=="no enriched GO"] # remove "no enriched GO" result
    ## add sample info and FC info and save GO.ORA result
        if(length(x)==0) {next} else {GO.ORA.result<-x}
GO.ORA.result      
## $GO.ORA.temp.up
##        category over_represented_pvalue under_represented_pvalue numDEInCat
## 1210 GO:0010200            1.357094e-12                1.0000000         36
## 2253 GO:0042742            1.061509e-10                1.0000000         61
## 890  GO:0009611            9.615647e-09                1.0000000         39
## 2750 GO:0050832            2.163094e-08                1.0000000         39
## 899  GO:0009626            3.350053e-08                1.0000000         21
## 638  GO:0006952            7.956456e-08                1.0000000         75
## 853  GO:0009407            7.000843e-07                0.9999999         11
## 900  GO:0009627            9.893457e-07                0.9999998         15
## 1174 GO:0010120            2.987504e-06                0.9999998          8
## 894  GO:0009617            3.027497e-06                0.9999991         24
## 557  GO:0006749            4.127199e-06                0.9999994         12
## 646  GO:0006979            4.499773e-06                0.9999982         36
## 3708 GO:2000022            5.272435e-06                0.9999991         13
## 1166 GO:0010112            5.493947e-06                0.9999996          7
## 423  GO:0006468            6.010503e-06                0.9999967         91
## 2859 GO:0051707            1.635476e-05                0.9999968         13
## 972  GO:0009751            1.886256e-05                0.9999932         27
## 1038 GO:0009871            1.984908e-05                0.9999993          5
## 3442 GO:1900067            4.006062e-05                1.0000000          3
## 1107 GO:0010030            4.605592e-05                0.9999934          9
## 855  GO:0009409            5.161047e-05                0.9999755         42
## 3164 GO:0071732            5.481625e-05                0.9999920          9
## 898  GO:0009625            6.533906e-05                0.9999874         11
## 1858 GO:0031348            9.920065e-05                0.9999821         10
## 3114 GO:0071369            1.327728e-04                0.9999777          9
## 607  GO:0006869            1.391666e-04                0.9999608         15
## 2986 GO:0062034            1.434714e-04                0.9999954          4
## 1183 GO:0010150            1.702460e-04                0.9999427         19
## 2917 GO:0055114            1.965588e-04                0.9998735         96
## 49   GO:0000272            2.534934e-04                0.9999663          7
## 921  GO:0009651            2.650096e-04                0.9998502         56
## 2439 GO:0045332            2.706706e-04                0.9999723          6
## 478  GO:0006562            2.881153e-04                0.9999969          3
## 185  GO:0002229            3.712637e-04                0.9998926         14
## 3094 GO:0071281            4.180861e-04                0.9999083         10
##      numInCat
## 1210      286
## 2253      726
## 890       419
## 2750      469
## 899       140
## 638      1165
## 853        67
## 900       104
## 1174       27
## 894       241
## 557        85
## 646       502
## 3708       89
## 1166       22
## 423      1484
## 2859       97
## 972       347
## 1038       11
## 3442        3
## 1107       54
## 855       696
## 3164       52
## 898        84
## 1858       64
## 3114       62
## 607       208
## 2986        8
## 1183      219
## 2917     1923
## 49         39
## 921      1045
## 2439       23
## 478         4
## 185       126
## 3094       77
##                                                                                               term
## 1210                                                                            response to chitin
## 2253                                                                 defense response to bacterium
## 890                                                                           response to wounding
## 2750                                                                    defense response to fungus
## 899                                                             plant-type hypersensitive response
## 638                                                                               defense response
## 853                                                                        toxin catabolic process
## 900                                                                   systemic acquired resistance
## 1174                                                                camalexin biosynthetic process
## 894                                                                          response to bacterium
## 557                                                                  glutathione metabolic process
## 646                                                                   response to oxidative stress
## 3708                                        regulation of jasmonic acid mediated signaling pathway
## 1166                                                    regulation of systemic acquired resistance
## 423                                                                        protein phosphorylation
## 2859                                                                    response to other organism
## 972                                                                     response to salicylic acid
## 1038 jasmonic acid and ethylene-dependent systemic resistance, ethylene mediated signaling pathway
## 3442                                                regulation of cellular response to alkaline pH
## 1107                                                       positive regulation of seed germination
## 855                                                                               response to cold
## 3164                                                             cellular response to nitric oxide
## 898                                                                             response to insect
## 1858                                                       negative regulation of defense response
## 3114                                                        cellular response to ethylene stimulus
## 607                                                                                lipid transport
## 2986                                                         L-pipecolic acid biosynthetic process
## 1183                                                                               leaf senescence
## 2917                                                                   oxidation-reduction process
## 49                                                                polysaccharide catabolic process
## 921                                                                        response to salt stress
## 2439                                                                    phospholipid translocation
## 478                                                                      proline catabolic process
## 185                                                                  defense response to oomycetes
## 3094                                                                 cellular response to iron ion
##      ontology over_represented_padjust
## 1210       BP             5.142029e-09
## 2253       BP             2.011029e-07
## 890        BP             1.214456e-05
## 2750       BP             2.048991e-05
## 899        BP             2.538670e-05
## 638        BP             5.024502e-05
## 853        BP             3.789456e-04
## 900        BP             4.685789e-04
## 1174       BP             1.147119e-03
## 894        BP             1.147119e-03
## 557        BP             1.420803e-03
## 646        BP             1.420803e-03
## 3708       BP             1.486897e-03
## 1166       BP             1.486897e-03
## 423        BP             1.518253e-03
## 2859       BP             3.873011e-03
## 972        BP             4.178232e-03
## 1038       BP             4.178232e-03
## 3442       BP             7.988931e-03
## 1107       BP             8.725295e-03
## 855        BP             9.312003e-03
## 3164       BP             9.440854e-03
## 898        BP             1.076390e-02
## 1858       BP             1.566130e-02
## 3114       BP             2.012305e-02
## 607        BP             2.013382e-02
## 2986       BP             2.013382e-02
## 1183       BP             2.303794e-02
## 2917       BP             2.568143e-02
## 49         BP             3.201621e-02
## 921        BP             3.204910e-02
## 2439       BP             3.204910e-02
## 478        BP             3.308087e-02
## 185        BP             4.137407e-02
## 3094       BP             4.526081e-02
##                                                                                               Term
## 1210                                                                            response to chitin
## 2253                                                                 defense response to bacterium
## 890                                                                           response to wounding
## 2750                                                                    defense response to fungus
## 899                                                             plant-type hypersensitive response
## 638                                                                               defense response
## 853                                                                        toxin catabolic process
## 900                                                                   systemic acquired resistance
## 1174                                                                camalexin biosynthetic process
## 894                                                                          response to bacterium
## 557                                                                  glutathione metabolic process
## 646                                                                   response to oxidative stress
## 3708                                        regulation of jasmonic acid mediated signaling pathway
## 1166                                                    regulation of systemic acquired resistance
## 423                                                                        protein phosphorylation
## 2859                                                                    response to other organism
## 972                                                                     response to salicylic acid
## 1038 jasmonic acid and ethylene-dependent systemic resistance, ethylene mediated signaling pathway
## 3442                                                regulation of cellular response to alkaline pH
## 1107                                                       positive regulation of seed germination
## 855                                                                               response to cold
## 3164                                                             cellular response to nitric oxide
## 898                                                                             response to insect
## 1858                                                       negative regulation of defense response
## 3114                                                        cellular response to ethylene stimulus
## 607                                                                                lipid transport
## 2986                                                         L-pipecolic acid biosynthetic process
## 1183                                                                               leaf senescence
## 2917                                                                   oxidation-reduction process
## 49                                                                polysaccharide catabolic process
## 921                                                                        response to salt stress
## 2439                                                                    phospholipid translocation
## 478                                                                      proline catabolic process
## 185                                                                  defense response to oomycetes
## 3094                                                                 cellular response to iron ion
##                                                                                                                                                                                                                                                                                                                                                                                  Definition
## 1210                                                                                                                                                                                         A process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chitin stimulus.
## 2253                                                                                                                                                                                                                                                                               Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
## 890                                                                                                                                                             Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
## 2750                                                                                                                                                                                                                                                                                  Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
## 899                                                                                                                                                                                                                                                                                                        The rapid, localized death of plant cells in response to invasion by a pathogen.
## 638                                                                                                                                                       Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
## 853                                                                                                                                          The chemical reactions and pathways resulting in the breakdown of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.
## 900                                                                                                                                                                                                                                                                                             The salicylic acid mediated response to a pathogen which confers broad spectrum resistance.
## 1174                                                                                                                                                                                                                                                                                    The chemical reactions and pathways resulting in the formation of camalexin, an indole phytoalexin.
## 894                                                                                                                                                                              Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
## 557  The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
## 646                               Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
## 3708                                                                                                                                                                                                                                                                                  Any process that modulates the frequency, rate or extent of jasmonic acid mediated signaling pathway.
## 1166                                                                                                                                                                                                                                                                                              Any process that modulates the frequency, rate or extent of systemic acquired resistance.
## 423                                                                                                                                                                                                                                                                                                                           The process of introducing a phosphate group on to a protein.
## 2859                                                                                                                                                                 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism.
## 972                                                                                                                                                                                Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a salicylic acid stimulus.
## 1038                                                                                                                                                                                                                                                        The series of molecular signals mediated by ethylene (ethene) involved in jasmonic acid/ethylene dependent systemic resistance.
## 3442                                                                                                                                                                                                                                                                                                                                                                                   <NA>
## 1107                                                                                                                                                                                                                                                                                                                   Any process that activates or increase the rate of seed germination.
## 855                                                                                                                  Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
## 3164                                                                                                                                                                                                Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus.
## 898                                                                                                                                                                                Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from an insect.
## 1858                                                                                                                                                                                                                                                                                      Any process that stops, prevents, or reduces the frequency, rate or extent of a defense response.
## 3114                                                                                                                                                                                          Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethylene (ethene) stimulus.
## 607                                                                                                                                                 The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
## 2986                                                                                                                                                                                                                                                                            The chemical reactions and pathways resulting in the formation of L-pipecolic acid, a metabolite of lysine.
## 1183                                                                                                                                                                     The process that occurs in a leaf near the end of its active life that is associated with the dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism.
## 2917                                                                                                                                                                                               A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
## 49                                                                                                                                                                                                            The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
## 921                                                Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
## 2439                                                                                                                                                                                                                                                                                The movement of a phospholipid molecule from one leaflet of a membrane bilayer to the opposite leaflet.
## 478                                                                                                                                                                                        The chemical reactions and pathways resulting in the breakdown of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
## 185                                                                                                                                                                                                                                                                                  Reactions triggered in response to the presence of oomycetes that act to protect the cell or organism.
## 3094                                                                                                                                                                                                   Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an iron ion stimulus.
# save data           
save(GO.ORA.result,file="../output/GOseq.timecourse.twoafternoon.Brgo.v3.0.Atgoslim.BP.list.enrich.Rdata")

session info

sessionInfo
## function (package = NULL) 
## {
##     z <- list()
##     z$R.version <- R.Version()
##     z$platform <- z$R.version$platform
##     if (nzchar(.Platform$r_arch)) 
##         z$platform <- paste(z$platform, .Platform$r_arch, sep = "/")
##     z$platform <- paste0(z$platform, " (", 8 * .Machine$sizeof.pointer, 
##         "-bit)")
##     z$locale <- Sys.getlocale()
##     z$running <- osVersion
##     z$RNGkind <- RNGkind()
##     if (is.null(package)) {
##         package <- grep("^package:", search(), value = TRUE)
##         keep <- vapply(package, function(x) x == "package:base" || 
##             !is.null(attr(as.environment(x), "path")), NA)
##         package <- .rmpkg(package[keep])
##     }
##     pkgDesc <- lapply(package, packageDescription, encoding = NA)
##     if (length(package) == 0) 
##         stop("no valid packages were specified")
##     basePkgs <- sapply(pkgDesc, function(x) !is.null(x$Priority) && 
##         x$Priority == "base")
##     z$basePkgs <- package[basePkgs]
##     if (any(!basePkgs)) {
##         z$otherPkgs <- pkgDesc[!basePkgs]
##         names(z$otherPkgs) <- package[!basePkgs]
##     }
##     loadedOnly <- loadedNamespaces()
##     loadedOnly <- loadedOnly[!(loadedOnly %in% package)]
##     if (length(loadedOnly)) {
##         names(loadedOnly) <- loadedOnly
##         pkgDesc <- c(pkgDesc, lapply(loadedOnly, packageDescription))
##         z$loadedOnly <- pkgDesc[loadedOnly]
##     }
##     z$matprod <- as.character(options("matprod"))
##     es <- extSoftVersion()
##     z$BLAS <- as.character(es["BLAS"])
##     z$LAPACK <- La_library()
##     class(z) <- "sessionInfo"
##     z
## }
## <bytecode: 0x7fcf2d6aee40>
## <environment: namespace:utils>